Jmol now generates isosurfaces from scalar field data from files in the
gaussuain .cube format.
The 'load' command only reads the atom position data from the .cube file.
A separate 'isosurface' command is used to read the scalar field data and
construct the isosurface.
Parameters to the 'isosurface' command control the construction of the
surface. By reading the same .cube file more than once with different
parameters, or by reading different .cube files, once can construct
different isosurfaces with different shapes and sizes. By naming these
individual surfaces with an identifier one can control display settings
and color for each of the surfaces independently.
The 'isosurface' command is similar to the 'pmesh' command in usage and
parameters.
isosurface <arguments>
all arguments are optional ... but use combinations that make sense
isosurfaceID
------------
an optional alphanumeric identifier used to identify this surface
cutoff
------
floating point value used as isosurface cutoff. If cutoff is positive then
values >= cutoff are inside. If cutoff is negative then values <= cutoff
are inside. Default is currently 0.02. Note that positive and negative
surfaces are created separately so that one can give them distinct names
and control their display properties independently.
dots | nodots
-------------
turn on/off display of dots at the points. defaults to nodots
mesh | nomesh
-------------
turn on/off display of the triangular mesh. defaults to nomesh
fill | nofill
-------------
turn on/off filling of the surface. defaults to fill
"path/to/filename.cube"
-----------------------
path name to your gaussian .cube file. This *must* be in double quotes (as
with the pmesh command).
on | off
--------
Turns on/off the display of the surface
delete
------
deletes the specified isosurface
coloring:
color isosurface {translucent|opaque} <colorValue>
the combination of opaque, translucent, mesh, and dots gives flexibility
in showing multiple layers and/or surfaces of different types around the
same molecule.
Notes:
1. Generally, if a name is provided then the command only applies to that
particular isosurface. If no name is provided then it applies to all the
isosurfaces.
2. As with other files, .cube files may be compressed using gzip.
Example:
load "samples/cube/benzene-homo.cub.gz"; # just load the molecule
isosurface pos05 0.05 "samples/cube/benzene-homo.cub.gz";
isosurface neg05 -0.05 "samples/cube/benzene-homo.cub.gz";
# now load some other surface further out
isosurface pos01 0.01 "samples/cube/benzene-homo.cub.gz";
isosurface neg01 -0.01 "samples/cube/benzene-homo.cub.gz";
color isosurface translucent; # make neg01 translucent
isosurface pos01 nofill mesh; # make pos01 a mesh
color isosurface translucent; # make the pos01 mesh translucent too
isosurface neg01 dots; # make neg01 show dots too
isosurface neg01 nofill; # only dots
isosurface nodots nomesh fill; #everybody is back to a solid ...
color isosurface opaque; # ... and opaque
isosurface neg01; #select neg01
color isosurface green;
isosurface pos01;
color isosurface violet;
slab on; slab 50; # slab in order to see the inside
slab off; # we're done ... Wasn't that fun?!
-----
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